PDBsum entry 1gpu

Transferase

PDB id: 1gpu

Contents

Protein chains

678 a.a. *

Ligands

THD ×2

Metals

_CA ×2

Waters ×859

* Residue conservation analysis

PDB id:

1gpu

Name:

Transferase

Title:

Transketolase complex with reaction intermediate

Structure:

Transketolase 1. Chain: a, b. Synonym: tk 1. Ec: 2.2.1.1

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Biol. unit:

Dimer (from PDB file)

Resolution:

1.86Å R-factor: 0.198 R-free: 0.225

Authors:

E.Fiedler,S.Thorell,T.Sandalova,S.Koenig,G.Schneider

Key ref:

E.Fiedler et al. (2002). Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the alpha-carbanion of (alpha,beta-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae. Proc Natl Acad Sci U S A, 99, 591-595. PubMed id: 11773632 DOI: 10.1073/pnas.022510999

Date:

09-Nov-01 Release date: 11-Feb-02

Protein chains

P23254  (TKT1_YEAST) -  Transketolase 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 680 a.a.

Struc: 678 a.a.

Enzyme reactions

• Enzyme class: E.C.2.2.1.1 - transketolase.
• Reaction: D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = aldehydo-D- ribose 5-phosphate + D-xylulose 5-phosphate
• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = THD) matches with 86.67% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.022510999

Proc Natl Acad Sci U S A 99:591-595 (2002)

PubMed id: 11773632

Snapshot of a key intermediate in enzymatic thiamin catalysis: crystal structure of the alpha-carbanion of (alpha,beta-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae.

E.Fiedler, S.Thorell, T.Sandalova, R.Golbik, S.König, G.Schneider.

ABSTRACT

Kinetic and spectroscopic data indicated that addition of the donor substrate hydroxypyruvate to the thiamin diphosphate (ThDP)-dependent enzyme transketolase (TK) led to the accumulation of the alpha-carbanion/enamine of (alpha,beta-dihydroxyethyl) ThDP, the key reaction intermediate in enzymatic thiamin catalysis. The three-dimensional structure of this intermediate trapped in the active site of yeast TK was determined to 1.9-A resolution by using cryocrystallography. The electron density suggests a planar alpha-carbanion/enamine intermediate having the E-configuration. The reaction intermediate is firmly held in place through direct hydrogen bonds to His-103 and His-481 and an indirect hydrogen bond via a water molecule to His-69. The 4-NH(2) group of the amino-pyrimidine ring of ThDP is within 3 A distance to the alpha-hydroxy oxygen atom of the dihydroxyethyl moiety but at an angle unfavorable for a strong hydrogen bond. No structural changes occur in TK on formation of the reaction intermediate, suggesting that the active site is poised for catalysis and conformational changes during the enzyme reaction are not very likely. The intermediate is present with high occupancy in both active sites, arguing against previous proposals of half-of-the-sites reactivity in yeast TK.

Selected figure(s)

Figure 1.
Fig. 1. Formation of the -carbanion/enamine intermediate by using HPA as donor substrate.

Figure 5.
Fig. 5. Superposition of the ThDP molecule bound in holoTK with the covalent reaction intermediate DHEThDP in the TK-intermediate complex. The superposition is based on 678 C atoms of the TK subunit.

Figures were selected by an automated process.